annotate mgescan.xml @ 6:f65687bfdc0a draft

Uploaded
author hyungrolee
date Mon, 15 Feb 2016 03:33:33 -0500
parents 7658ef159fd8
children 106ee0841650
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
1 <?xml version="1.0"?>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
2
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
3 <tool name="MGEScan" id="mgescan" version="0.0.2">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
4 <description>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
5 MGEScan
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
6 </description>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
7 <requirements>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
8 <requirement type="package" version="3.0">mgescan</requirement>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
9 </requirements>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
10 <version_command>mgescan --version</version_command>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
11 <command interpreter="bash">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
12 mgescan.sh $input '$input.name' 3 $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 $both_gff3 $mpi_yn.nmpi
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
13 <!-- mgescan.sh $input $input.name $hmmver $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 -->
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
14 </command>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
15 <inputs>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
16 <param format="fasta,tabular,data" name="input" type="data" label="Input FASTA file(s)"/>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
17 <!--param name="hmmver" type="select" label="Hmmsearch version">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
18 <option selected="selected" value="3">3</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
19 <option value="2">2</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
20 </param-->
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
21 <param name="program" type="select" label="MGEScan">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
22 <option selected="selected" value="B">Both</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
23 <option value="L">LTR</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
24 <option value="N">nonLTR</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
25 </param>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
26 <conditional name="mpi_yn">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
27 <param name="mpi_select" type="select" label="Enable MPI">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
28 <option value="no_mpi">No</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
29 <option value="yes_mpi">Yes</option>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
30 </param>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
31 <when value="yes_mpi">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
32 <param name="nmpi" format="txt" type="text" value="1" label="Number of MPI Processes"/>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
33 </when>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
34 <when value="no_mpi">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
35 <param name="nmpi" type="hidden" value="0"/>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
36 </when>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
37 </conditional>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
38 </inputs>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
39 <outputs>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
40 <data format="ltr.out" name="output" label="LTR Results (ltr.out)">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
41 <filter>program != "N"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
42 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
43 <data format="fasta" name="clade" label="clade file (FASTA)">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
44 <filter>program != "L"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
45 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
46 <data format="qfile" name="qvalue_en" label="qvalue_en">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
47 <filter>program != "L"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
48 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
49 <data format="qfile" name="qvalue_rt" label="qvalue_rt">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
50 <filter>program != "L"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
51 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
52 <data format="gff3" name="ltr_gff3" label="GFF3 for LTR">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
53 <filter>program != "N"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
54 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
55 <data format="gff3" name="nonltr_gff3" label="GFF3 for nonLTR">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
56 <filter>program != "L"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
57 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
58 <data format="gff3" name="both_gff3" label="GFF3 for LTR and nonLTR">
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
59 <filter>program == "B"</filter>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
60 </data>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
61
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
62 </outputs>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
63 <help>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
64 How to Run MGEScan
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
65 ===================
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
66
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
67 * Select an input genome data from the select box, and choose a program. Both LTR and nonLTR of MGEScan is default.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
68 * Click 'Execute' button.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
69 * MPI will be enabled depending on your system support.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
70
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
71 If you like to have more options to run LTR or nonLTR program, use separated tools on the left panel.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
72
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
73 For example, in LTR > MGEScan-LTR, preprocessing by repeatmasker and setting other variables are available e.g. distance(bp) between LTRs.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
74
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
75 Output
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
76 ============
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
77
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
78 A. MGEScan_LTR:
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
79
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
80 Upon completion, MGEScan-LTR generates a file "ltr.out". This output file has information
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
81 about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
82 retrotransposons starts with the head line of "[cluster_number]---------", followed by
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
83 the information of LTR retrotransposons in the cluster. The columns for LTR
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
84 retrotransposons are as follows.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
85
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
86 1. LTR_id: unique id of LTRs identified. It consist of two components, sequence file name and id in the file. For example, chr1_2 is the second LTR retrotransposon in the chr1 file.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
87 2. start position of 5’ LTR.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
88 3. end position of 5’ LTR.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
89 4. start position of 3’ LTR.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
90 5. end position of 3’ LTR.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
91 6. strand: + or -.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
92 7. length of 5’ LTR.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
93 8. length of 3’ LTR.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
94 9. length of the LTR retrotransposon.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
95 10. TSD on the left side of the LTR retotransposons.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
96 11. TSD on the right side of the LTR retrotransposons.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
97 12. di(tri)nucleotide on the left side of 5’LTR
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
98 13. di(tri)nucleotide on the right side of 5’LTR
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
99 14. di(tri)nucleotide on the left side of 3’LTR
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
100 15. di(tri)nucleotide on the right side of 3’LTR
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
101
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
102 B. MGEScan_nonLTR:
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
103 Upon completion, MGEScan-nonLTR generates the directory, "info" in the data directory you
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
104 specified. In this "info" directory, two sub-directories ("full" and "validation") are
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
105 generated.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
106
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
107 * The "full" directory is for storing sequences of elements. Each subdirectory in "full"
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
108 is the name of clade. In each directory of clade, the DNA sequences of nonLTRs identified
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
109 are listed. Each sequence is in fasta format. The header contains the position
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
110 information of TEs identified: [genome_file_name]_[start position in the sequence]
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
111
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
112 For example, >chr1_333 means that this element start at 333bp in the "chr1" file.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
113
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
114 * The "validation" directory is for storing Q values.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
115 In the files "en" and "rt", the first column corresponds to the element name and the last column Q value.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
116
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
117 License
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
118 ============
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
119 Copyright 2015.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
120 You may redistribute this software under the terms of the GNU General Public License.
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
121
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
122 </help>
7658ef159fd8 Uploaded
hyungrolee
parents:
diff changeset
123 </tool>